Clinical-Genomics
[Bug] Variants not in expected sort order
Describe the bug Teresita sent in a ticket where she flagged that she doesn't recognise the sort order of the variants in the file SNV.somatic.XXXXXXXXX.vardict.vcf.gz (case name removed). More info in the ticket
Karl Svärd thought perhaps that this is due to it being a WES case?
To Reproduce
Expected behavior
If workflow, which rules
Screenshots
Version (please complete the following information): 12
Additional context We need to make sure to answer her back in the ticket.
I replied in the ticket. Pasting my response below: It seems that an intermediate process disrupts the sort order, we can add a final sort command to make sure that the VCF is sorted.
Is this something that has changed recently? If it is then I think it makes sense to try to fix this so it doesn't cause confusion. If not, then I got the impression from the ticket that this was not an issue.
Added this to the 13 release just so we don't forget about it. Could be 14 if it's too much work
Never fixed, and now we are replacing vardict with tnscope. Closing the issue and removing from milestone and board
